| Previous changeset 20:f3a219de2d1b (2019-06-13) Next changeset 22:638dcd2d93bc (2019-06-14) |
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Commit message:
planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5-dirty |
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modified:
toolRPViz.py |
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added:
rpviz_on_data_1_html.html |
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removed:
outfile.html |
| b |
| diff -r f3a219de2d1b -r cb029043c1d6 outfile.html --- a/outfile.html Thu Jun 13 09:00:26 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,139 +0,0 @@\n-<!DOCTYPE doctype html>\n-<html>\n- <head>\n- <meta charset="utf-8"/>\n- <title>\n- Viewer\n- </title>\n- <script id="elements">\n- var obj ={"rp_2": {"nodes": [{"data": {"category": "reactions", "id": "<Reaction RP1>", "value": "<Reaction RP1>", "name": "<Reaction RP1>"}}, {"data": {"category": "reactions", "id": "<Reaction RP0>", "value": "<Reaction RP0>", "name": "<Reaction RP0>"}}, {"data": {"category": "reactions", "id": "<Reaction targetSink>", "value": "<Reaction targetSink>", "name": "<Reaction targetSink>"}}, {"data": {"category": "reactant", "name": "anthranilate", "link": "http://identifiers.org/metanetx.chemical/MNXM188", "root": "root", "id": "MNXM188__64__MNXC3", "value": "MNXM188__64__MNXC3"}}, {"data": {"category": "reactant", "name": "O2", "link": "http://identifiers.org/metanetx.chemical/MNXM4", "root": "root", "id": "MNXM4__64__MNXC3", "value": "MNXM4__64__MNXC3"}}, {"data": {"category": "reactant", "name": "NADPH", "link": "http://identifiers.org/metanetx.chemical/MNXM6", "root": "root", "id": "MNXM6__64__MNXC3", "value": "MNXM6__64__MNXC3"}}, {"data": {"category": "product", "smiles": "[H]Oc1c([H])c([H])c([H])c([H])c1O[H]", "image": "<svg version=\'1.1\' baseProfile=\'full\'\\n xmlns=\'http://www.w3.org/2000/svg\'\\n xmlns:rdkit=\'http://www.rdkit.org/xml\'\\n xmlns:xlink=\'http://www.w3.org/1999/xlink\'\\n xml:space=\'preserve\'\\nwidth=\'200px\' height=\'200px\' >\\n<!-- END OF HEADER -->\\n<rect style=\'opacity:1.0;fill:#FFFFFF;stroke:none\' width=\'200\' height=\'200\' x=\'0\' y=\'0\'> </rect>\\n<path class=\'bond-0\' d=\'M 140.376,147.373 123.965,137.899\' style=\'fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-0\' d=\'M 123.965,137.899 107.555,128.424\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-1\' d=\'M 107.555,128.424 58.3228,156.848\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-1\' d=\'M 94.4851,122.841 60.0228,142.738\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'bond-7\' d=\'M 107.555,128.424 107.555,71.576\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-7\' d=\'M 96.1851,119.897 96.1851,80.1032\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'bond-2\' d=\'M 58.3228,156.848 9.09091,128.424\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-2\' d=\'M 56.6228,142.738 22.1605,122.841\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'bond-3\' d=\'M 9.09091,128.424 9.09091,71.576\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-3\' d=\'M 20.4605,119.897 20.4605,80.1032\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'bond-4\' d=\'M 9.09091,71.576 58.3228,43.1519\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-4\' d=\'M 22.1605,77.1587 56.6228,57.2619\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'b'..b'", "target": "CMPD_0000000049__64__MNXC3"}}, {"data": {"source": "<Reaction RP3>", "target": "CMPD_0000000029__64__MNXC3"}}, {"data": {"source": "<Reaction RP2>", "target": "CMPD_0000000012__64__MNXC3"}}, {"data": {"source": "<Reaction RP1>", "target": "CMPD_0000000003__64__MNXC3"}}, {"data": {"source": "<Reaction RP0>", "target": "TARGET_0000000001__64__MNXC3"}}, {"data": {"source": "MNXM164__64__MNXC3", "target": "<Reaction RP4>"}}, {"data": {"source": "MNXM6__64__MNXC3", "target": "<Reaction RP4>"}}, {"data": {"source": "CMPD_0000000049__64__MNXC3", "target": "<Reaction RP3>"}}, {"data": {"source": "MNXM4__64__MNXC3", "target": "<Reaction RP3>"}}, {"data": {"source": "MNXM4__64__MNXC3", "target": "<Reaction RP0>"}}, {"data": {"source": "CMPD_0000000029__64__MNXC3", "target": "<Reaction RP2>"}}, {"data": {"source": "MNXM2__64__MNXC3", "target": "<Reaction RP2>"}}, {"data": {"source": "CMPD_0000000012__64__MNXC3", "target": "<Reaction RP1>"}}, {"data": {"source": "CMPD_0000000003__64__MNXC3", "target": "<Reaction RP0>"}}, {"data": {"source": "TARGET_0000000001__64__MNXC3", "target": "<Reaction targetSink>"}}]}}\n- </script>\n- <script id="svg">\n- </script>\n- <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js">\n- </script>\n- <script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.0/cytoscape.min.js">\n- </script>\n- <script>\n- function displaynet(network){\n- var cy = cytoscape({\n- container: $(\'#cy\'),\n-\n- elements:network\n- ,\n-\n- layout: {\n- name: \'breadthfirst\',\n- roots: "node[root = \'root\']"\n- },\n-\n- style: [\n- {\n- selector: "node",\n- style: {\n- "background-color": \'#80D0D0\',\n- "label": "data(name)",\n- "font-size": "7px"\n- }\n- },\n- {selector: "node[category=\'reactions\']",\n- style: {\n- \'background-color\': \'#FA8072\',\n- \'shape\': \'roundrectangle\'\n- }},\n- {selector: "node[category=\'reactant\']",\n- style: {\n- \'background-color\': \'#52be80\',\n- }},\n- {\n- selector: \'edge\',\n- style: {\n- \'curve-style\': \'bezier\',\n- \'width\': \'3px\',\n- \'target-arrow-shape\': \'triangle\',\n- }\n- }]\n- });\n-\n- cy.on(\'mouseover\',\'node\',function(e){\n- var node_select=e.target;\n- molecule=node_select.data("image");\n- if(molecule){\n- $("#molecule").append(molecule)};\n- });\n-\n- cy.on(\'mouseout\',\'node\',function(e){\n- $("#molecule").empty();\n- });\n-\n- cy.on(\'tap\',\'node\',function(e){\n- var node_select=e.target;\n- console.log(node_select.data("name"));\n- link=node_select.data("link");\n- if(link){\n- window.open(link)\n- };\n- });\n- };\n-\n- $(function() {\n- $("#selectbox").change(function(){\n- value=$("#selectbox :selected").val();\n- displaynet(obj[value]);\n- });\n- });\n- </script>\n- </head>\n- <style>\n- #cy {\n- width: 80%;\n- height: 100%;\n- position: absolute;\n- left : 20%;\n- }\n-\n-.interact{\n- position:relative;\n- width: 19%;\n- height:100%;\n-}\n-#molecule{\n- position : absolute;\n- top : 80px;\n-}\n- </style>\n- <body>\n- <div id="cy">\n- </div>\n- <div class="interact" id="interaction">\n- <div id="molecule">\n- </div>\n- <form>\n- Choose a pathway :\n- <select id="selectbox">\n- <option value="select">\n- Select a pathway\n- </option>\n- <option value="rp_2">\n- rp_2\n- </option>\n- <option value="rp_3">\n- rp_3\n- </option>\n- <option value="rp_4">\n- rp_4\n- </option>\n- <option value="rp_63">\n- rp_63\n- </option>\n- <option value="rp_64">\n- rp_64\n- </option>\n- <option value="rp_65">\n- rp_65\n- </option>\n- </select>\n- </form>\n- </div>\n- </body>\n-</html>\n' |
| b |
| diff -r f3a219de2d1b -r cb029043c1d6 rpviz_on_data_1_html.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz_on_data_1_html.html Thu Jun 13 09:52:15 2019 -0400 |
| [ |
| b'@@ -0,0 +1,139 @@\n+<!DOCTYPE doctype html>\n+<html>\n+ <head>\n+ <meta charset="utf-8"/>\n+ <title>\n+ Viewer\n+ </title>\n+ <script id="elements">\n+ var obj ={"rp_2": {"nodes": [{"data": {"category": "reactions", "id": "<Reaction RP1>", "value": "<Reaction RP1>", "name": "<Reaction RP1>"}}, {"data": {"category": "reactions", "id": "<Reaction RP0>", "value": "<Reaction RP0>", "name": "<Reaction RP0>"}}, {"data": {"category": "reactions", "id": "<Reaction targetSink>", "value": "<Reaction targetSink>", "name": "<Reaction targetSink>"}}, {"data": {"category": "reactant", "name": "anthranilate", "link": "http://identifiers.org/metanetx.chemical/MNXM188", "root": "root", "id": "MNXM188__64__MNXC3", "value": "MNXM188__64__MNXC3"}}, {"data": {"category": "reactant", "name": "O2", "link": "http://identifiers.org/metanetx.chemical/MNXM4", "root": "root", "id": "MNXM4__64__MNXC3", "value": "MNXM4__64__MNXC3"}}, {"data": {"category": "reactant", "name": "NADPH", "link": "http://identifiers.org/metanetx.chemical/MNXM6", "root": "root", "id": "MNXM6__64__MNXC3", "value": "MNXM6__64__MNXC3"}}, {"data": {"category": "product", "smiles": "[H]Oc1c([H])c([H])c([H])c([H])c1O[H]", "image": "<svg version=\'1.1\' baseProfile=\'full\'\\n xmlns=\'http://www.w3.org/2000/svg\'\\n xmlns:rdkit=\'http://www.rdkit.org/xml\'\\n xmlns:xlink=\'http://www.w3.org/1999/xlink\'\\n xml:space=\'preserve\'\\nwidth=\'200px\' height=\'200px\' >\\n<!-- END OF HEADER -->\\n<rect style=\'opacity:1.0;fill:#FFFFFF;stroke:none\' width=\'200\' height=\'200\' x=\'0\' y=\'0\'> </rect>\\n<path class=\'bond-0\' d=\'M 140.376,147.373 123.965,137.899\' style=\'fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-0\' d=\'M 123.965,137.899 107.555,128.424\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-1\' d=\'M 107.555,128.424 58.3228,156.848\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-1\' d=\'M 94.4851,122.841 60.0228,142.738\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'bond-7\' d=\'M 107.555,128.424 107.555,71.576\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-7\' d=\'M 96.1851,119.897 96.1851,80.1032\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'bond-2\' d=\'M 58.3228,156.848 9.09091,128.424\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-2\' d=\'M 56.6228,142.738 22.1605,122.841\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'bond-3\' d=\'M 9.09091,128.424 9.09091,71.576\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-3\' d=\'M 20.4605,119.897 20.4605,80.1032\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'bond-4\' d=\'M 9.09091,71.576 58.3228,43.1519\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\' />\\n<path class=\'bond-4\' d=\'M 22.1605,77.1587 56.6228,57.2619\' style=\'fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\' />\\n<path class=\'b'..b'", "target": "CMPD_0000000049__64__MNXC3"}}, {"data": {"source": "<Reaction RP3>", "target": "CMPD_0000000029__64__MNXC3"}}, {"data": {"source": "<Reaction RP2>", "target": "CMPD_0000000012__64__MNXC3"}}, {"data": {"source": "<Reaction RP1>", "target": "CMPD_0000000003__64__MNXC3"}}, {"data": {"source": "<Reaction RP0>", "target": "TARGET_0000000001__64__MNXC3"}}, {"data": {"source": "MNXM164__64__MNXC3", "target": "<Reaction RP4>"}}, {"data": {"source": "MNXM6__64__MNXC3", "target": "<Reaction RP4>"}}, {"data": {"source": "CMPD_0000000049__64__MNXC3", "target": "<Reaction RP3>"}}, {"data": {"source": "MNXM4__64__MNXC3", "target": "<Reaction RP3>"}}, {"data": {"source": "MNXM4__64__MNXC3", "target": "<Reaction RP0>"}}, {"data": {"source": "CMPD_0000000029__64__MNXC3", "target": "<Reaction RP2>"}}, {"data": {"source": "MNXM2__64__MNXC3", "target": "<Reaction RP2>"}}, {"data": {"source": "CMPD_0000000012__64__MNXC3", "target": "<Reaction RP1>"}}, {"data": {"source": "CMPD_0000000003__64__MNXC3", "target": "<Reaction RP0>"}}, {"data": {"source": "TARGET_0000000001__64__MNXC3", "target": "<Reaction targetSink>"}}]}}\n+ </script>\n+ <script id="svg">\n+ </script>\n+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js">\n+ </script>\n+ <script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.0/cytoscape.min.js">\n+ </script>\n+ <script>\n+ function displaynet(network){\n+ var cy = cytoscape({\n+ container: $(\'#cy\'),\n+\n+ elements:network\n+ ,\n+\n+ layout: {\n+ name: \'breadthfirst\',\n+ roots: "node[root = \'root\']"\n+ },\n+\n+ style: [\n+ {\n+ selector: "node",\n+ style: {\n+ "background-color": \'#80D0D0\',\n+ "label": "data(name)",\n+ "font-size": "7px"\n+ }\n+ },\n+ {selector: "node[category=\'reactions\']",\n+ style: {\n+ \'background-color\': \'#FA8072\',\n+ \'shape\': \'roundrectangle\'\n+ }},\n+ {selector: "node[category=\'reactant\']",\n+ style: {\n+ \'background-color\': \'#52be80\',\n+ }},\n+ {\n+ selector: \'edge\',\n+ style: {\n+ \'curve-style\': \'bezier\',\n+ \'width\': \'3px\',\n+ \'target-arrow-shape\': \'triangle\',\n+ }\n+ }]\n+ });\n+\n+ cy.on(\'mouseover\',\'node\',function(e){\n+ var node_select=e.target;\n+ molecule=node_select.data("image");\n+ if(molecule){\n+ $("#molecule").append(molecule)};\n+ });\n+\n+ cy.on(\'mouseout\',\'node\',function(e){\n+ $("#molecule").empty();\n+ });\n+\n+ cy.on(\'tap\',\'node\',function(e){\n+ var node_select=e.target;\n+ console.log(node_select.data("name"));\n+ link=node_select.data("link");\n+ if(link){\n+ window.open(link)\n+ };\n+ });\n+ };\n+\n+ $(function() {\n+ $("#selectbox").change(function(){\n+ value=$("#selectbox :selected").val();\n+ displaynet(obj[value]);\n+ });\n+ });\n+ </script>\n+ </head>\n+ <style>\n+ #cy {\n+ width: 80%;\n+ height: 100%;\n+ position: absolute;\n+ left : 20%;\n+ }\n+\n+.interact{\n+ position:relative;\n+ width: 19%;\n+ height:100%;\n+}\n+#molecule{\n+ position : absolute;\n+ top : 80px;\n+}\n+ </style>\n+ <body>\n+ <div id="cy">\n+ </div>\n+ <div class="interact" id="interaction">\n+ <div id="molecule">\n+ </div>\n+ <form>\n+ Choose a pathway :\n+ <select id="selectbox">\n+ <option value="select">\n+ Select a pathway\n+ </option>\n+ <option value="rp_2">\n+ rp_2\n+ </option>\n+ <option value="rp_3">\n+ rp_3\n+ </option>\n+ <option value="rp_4">\n+ rp_4\n+ </option>\n+ <option value="rp_63">\n+ rp_63\n+ </option>\n+ <option value="rp_64">\n+ rp_64\n+ </option>\n+ <option value="rp_65">\n+ rp_65\n+ </option>\n+ </select>\n+ </form>\n+ </div>\n+ </body>\n+</html>\n' |
| b |
| diff -r f3a219de2d1b -r cb029043c1d6 toolRPViz.py --- a/toolRPViz.py Thu Jun 13 09:00:26 2019 -0400 +++ b/toolRPViz.py Thu Jun 13 09:52:15 2019 -0400 |
| b |
| @@ -37,15 +37,9 @@ h.write(html) print( 'Success!') -def testHTML(f, outfile): - content = open(f).read() - with open(outfile, 'w') as h: - outfile.write(content) - if __name__ == "__main__": parser = arguments() arg = parser.parse_args() assert os.path.exists(arg.infile) - testHTML( 'outfile.html', arg.outfile ) -# pathwayUpload( arg.infile, arg.outfile, arg.server ) + pathwayUpload( arg.infile, arg.outfile, arg.server ) |